Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization

Background. Hawthorn species (Crataegus L.; Rosaceae tribe Maleae) form a well-defined clade comprising five subgeneric groups readily distinguished using either molecular or morphological data. While multiple subsidiary groups (taxonomic sections, series) are recognized within some subgenera, the number of and relationships among species in these groups are subject to disagreement. Gametophytic apomixis and polyploidy are prevalent in the genus, and disagreement concerns whether and how apomictic genotypes should be recognized taxonomically. Recent studies suggest that many polyploids arise from hybridization between members of different infrageneric groups.Methods. We used target capture and high throughput sequencing to obtain nucleotide sequences for 257 nuclear loci and nearly complete chloroplast genomes from a sample of hawthorns representing all five currently recognized subgenera. Our sample is structured to include two examples of intersubgeneric hybrids and their putative diploid and tetraploid parents. We queried the alignment of nuclear loci directly for evidence of hybridization, and compared individual gene trees with each other, and with both the maximum likelihood plastome tree and the nuclear concatenated and multilocus coalescent-based trees. Tree comparisons provided a promising, if challenging (because of the number of comparisons involved) method for visualizing variation in tree topology. We found it useful to deploy comparisons based not only on tree-tree distances but also on a metric of tree-tree concordance that uses extrinsic information about the relatedness of the terminals in comparing tree topologies.Results. In addition to obtaining well-supported phylogenies from plastome sequences and from a minimum of 244 low copy-number nuclear loci, we have examined the impact of hybridization on our data. We corroborate earlier evidence for hybridization having taken place, taking into account also the occurrence of incomplete lineage sorting (ILS) and individual gene trees that may be, to a greater or lesser extent, spurious because they are built in part from chimeric or otherwise misassembled sequences.

背景：山楂属（Crataegus L.；蔷薇科苹果亚族Maleae）为一界定清晰的单系演化支，包含5个亚属类群，可通过分子或形态数据予以区分。尽管部分亚属内已划分出多个次级分类类群（组、系），但此类群内的物种类群数量及其亲缘关系仍存在学术争议。配子体无融合生殖（gametophytic apomixis）与多倍化现象在该属中普遍存在，而关于无融合生殖基因型应如何开展分类学界定，学界尚未形成统一共识。近期研究显示，多数多倍体类群源自不同属下类群成员间的杂交事件。方法：本研究采用目标捕获结合高通量测序技术，对覆盖当前公认全部5个亚属的山楂属样本进行测序，成功获取257个核基因座（nuclear loci）及近乎完整的叶绿体基因组（chloroplast genomes）序列。本次采样设置了2个亚属间杂交实例及其推定的二倍体、四倍体亲本样本。我们直接对核基因座的比对序列开展杂交信号检索，并对单基因树进行两两比较，同时将其与最大似然法（maximum likelihood）构建的质体基因组树、核基因串联序列树及多基因溯祖（coalescent）树进行比对分析。尽管因比对数量庞大而颇具挑战性，但树结构比较仍是可视化拓扑结构变异的有效手段。本研究采用的比较策略不仅基于树间距离，还引入了一种利用终端类群亲缘关系的外部信息来评估树拓扑一致性的指标，该策略被证实极具应用价值。结果：本研究不仅从质体基因组序列及至少244个低拷贝核基因座中获得了支持度较高的系统发育树，还分析了杂交事件对测序数据的影响。结合不完全谱系分选（incomplete lineage sorting, ILS）以及因部分序列嵌合或组装错误导致单基因树可能存在不同程度虚假性的情况，本研究验证了此前关于杂交事件发生的相关证据。